src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.io.DataSourceType;
   6 import jalview.io.FileFormat;
   7 import jalview.io.FormatAdapter;
   8 import jalview.ws.api.JobId;
   9 import jalview.ws.api.MultipleSequenceAlignmentI;
  10 import jalview.ws.params.ArgumentI;
  11 import jalview.ws.params.InvalidArgumentException;
  12 import jalview.ws.params.WsParamSetI;
  13
  14 import java.io.IOError;
  15 import java.io.IOException;
  16 import java.rmi.ServerError;
  17 import java.util.List;
  18
  19 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  20 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  21 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  22
  23 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  24 {
  25   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
  26     super(client, service, "Sequence Alignment");
  27     style = ServiceClient.MSAWSCLIENT;
  28   }
  29
  30   @Override
  31   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  32   {
  33     return super.submit(toalign, parameters, list);
  34   }
  35
  36   @Override
  37   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  38   {
  39     List<RemoteFile> files;
  40     try
  41     {
  42       files = client.getJobResults(jobId.getJobId());
  43       for (RemoteFile f : files)
  44       {
  45         if (f.getMimeType().equals("application/clustal"))
  46         {
  47           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
  48         }
  49         else if (f.getMimeType().equals("application/fasta"))
  50         {
  51           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
  52         }
  53       }
  54     } catch (IOException e)
  55     {
  56       throw new IOError(e);
  57     }
  58     return null;
  59   }
  60 }